X-133991764-A-T

Variant names:

• chrX-133991764-A-T
• rs7883190

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.483 in 110,019 control chromosomes in the GnomAD database, including 10,053 homozygotes. There are 15,362 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (10053 hom., 15362 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.483 AC: 53129 AN: 109966 Hom.: 10051 Cov.: 22 AF XY: 0.476 AC XY: 15347 AN XY: 32252

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.480

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.483 AC: 53133 AN: 110019 Hom.: 10053 Cov.: 22 AF XY: 0.475 AC XY: 15362 AN XY: 32315

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.479

Alfa AF: 0.560 Hom.: 4238

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	12
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7883190; hg19: chrX-133125791;